Protein polymorphisms, including ones detected by two-dimensional protein electrophoresis and DNA sequence polymorphisms are being used as molecular markers to locate genes responsible for alcoholism-associated behavioral differences. Non-random assortment of polymorphic and behavioral phenotypes is sought as evidence of genetic linkage in large families with alcoholism. The probability of establishing linkage is maximized by 1) studying large pedigrees with impulsivity/aggressivity as a prominent behavioral trait accompanying alcoholism and 2) using a larger panel of polymorphisms than has heretofore been available. We have examined protein polymorphisms by two-dimensional electrophoresis in population and family studies and thereby have expanded our panel of available autosomal polymorphic markers from 25 to approximately 50, increasing the fraction of the genome covered at a linkage distance of 10cM from 14% to 26%. Use of DNA probes specific for the Y-chromosome and, possibly, other specifically implicated geni loci further increases the probability of establishing linkage. Established fibroblast and lymphoblast cell lines provides a resource with which new polymorphic markers covering additional regions of the genome can be tested and for in vitro metabolic studies including the selection of mutant cell lines. Computer-assisted image analysis permits quantitation of several hundred proteins 1) in individuals for metabolic fingerprinting, 2) in specific brain regions of inbred animals with alcoholism-related genetic differences and 3) in cells cultured in vitro for the identification of specific mutations and patterns of metabolic alteration associated with the action of alcohol as a depressive and addictive agent.